I am creating an RDS instance using CloudFormation using this:
\"Resources\": { \"myDB\": { \"Type\": \"AWS::RDS::DBInstance\",
No, it's not possible. However, you could have an EC2 instance connect to your RDS instance to do it. I'd probably store a .sql file in S3 and use a cloud-init script on the EC2 instance to download the file and execute it.